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Add new training for scATAC-seq batch correction using SnapATAC2 #5061

Merged
merged 32 commits into from
Feb 28, 2025
Merged

Add new training for scATAC-seq batch correction using SnapATAC2 #5061

merged 32 commits into from
Feb 28, 2025

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timonschlegel
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Multi-sample batch correction SnapATAC2 tutorial

@github-actions github-actions bot added the faqs label Aug 2, 2024
@timonschlegel
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Please note I have fixed a spelling mistake in faqs/galaxy/histories_datasets_vs_collections.md. I hope it isn't a problem that I forgot to make a seperate PR for this change.

@timonschlegel timonschlegel marked this pull request as ready for review August 8, 2024 11:00
@timonschlegel timonschlegel requested a review from a team as a code owner August 8, 2024 11:00
@timonschlegel timonschlegel changed the title [Draft] Add new training for scATAC-seq batch correction using SnapATAC2 Add new training for scATAC-seq batch correction using SnapATAC2 Aug 8, 2024
@timonschlegel
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This training is now ready for review

shiltemann
shiltemann reviewed Sep 19, 2024
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Thanks @timonschlegel! I will leave the content review to the single cell experts, but this looks great from a technical point of view! Just a few minor comments inline :)

topics/single-cell/tutorials/scatac-batch-correction-snapatac2/workflows/main_workflow.ga
@@ -0,0 +1,1675 @@
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It would be great if you could add a workflow test: https://training.galaxyproject.org/training-material/faqs/gtn/gtn_workflow_testing.html

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thanks for the review! I'll add the test

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Hi @timonschlegel! Just checking: are you still able/planning to do this? Do you need help? Thanks!

@pavanvidem
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@dianichj @MarisaJL please review this. Some of its content (like general concepts) might be recycled for your new scRNA batch correction tutorials.

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Hi SPOC(kies)! How can we finish this PR so that it will be merged? @nomadscientist @pavanvidem @MarisaJL ?

@dianichj
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Hi @shiltemann! I'm done with the review, please let me know if you need anything else, otherwise feel free to merge the PR whenever you get a chance. Thanks a ton for all your help! 🚀 We really needed to get this merged! 🙌

@shiltemann shiltemann merged commit d8e7ce3 into galaxyproject:main Feb 28, 2025
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@shiltemann
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Thanks a lot for the great tutorial @timonschlegel! And thanks for the thorough review @dianichj!!

@pavanvidem
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thanks @dianichj and @shiltemann

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@dianichj dianichj dianichj requested changes

@shiltemann shiltemann shiltemann approved these changes

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@timonschlegel @pavanvidem @dianichj @shiltemann